Oryza sativa Japonica Group transcriptome sequencing. Oryza sativa Japonica Group strain:cv. Nipponbare

Phosphate starvation/sufficient rice seedling, root or shoot Pi-starvation or Pi-sufficient stresses responsible rice genes, including previously unannotated genes were identified by Illumina mRNA-seq technology. 53 million reads from Pi-starvation or Pi-sufficient root or shoot tissues were uniquely mapped to the rice genome, and these included 40574 RAP3 transcripts in root and 39748 RAP3 transcripts in shoot. We compared our mRNA-seq expression data with that from Rice 44K oligomicroarray, and about 95.5% (root) and 95.4% (shoot) transcripts supported by the array were confirmed expression both by the array and by mRNA-seq, Moreover, 11888 (root) and 11098 (shoot) RAP genes which were not supported by array, were evidenced expression with mRNA-seq. Furthermore, we discovered 8590 (root) and 8193 (shoot) previously unannotated transcripts upon Pi-starvation and/or Pi-sufficient.

本研究借助Illumina平台mRNA测序（mRNA-seq）技术，对磷饥饿与磷充足条件下的水稻幼苗开展分析，鉴定出响应无机磷酸盐（Pi）饥饿或Pi充足胁迫的水稻基因，其中包含此前未被注释的基因。从Pi饥饿或Pi充足处理的水稻根、茎组织中获取的5300万条测序读段（reads）被唯一比对到水稻基因组，其中根部涵盖40574个RAP3转录本，茎部涵盖39748个RAP3转录本。本研究将本次mRNA-seq获得的表达数据与水稻44K寡核苷酸芯片（Rice 44K oligomicroarray）的数据进行比对，结果显示，芯片检测到的转录本中，根部约95.5%、茎部约95.4%的转录本同时被芯片和mRNA-seq验证存在表达。此外，共有11888个根部RAP基因与11098个茎部RAP基因未被芯片检测到，但通过mRNA-seq证实了其表达。进一步研究发现，在Pi饥饿和/或Pi充足处理条件下，根部鉴定出8590个此前未被注释的转录本，茎部鉴定出8193个此前未被注释的转录本。